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Sample GSM7977989 Query DataSets for GSM7977989
Status Public on Apr 17, 2024
Title ChIP against H3K27me3 in E18.5 mouse male urogenital sinus replicate 1
Sample type SRA
 
Source name urogenital sinus
Organism Mus musculus
Characteristics tissue: urogenital sinus
Sex: male
Stage: E18.5
antibody: H3K27me3 (Merck Millipore, 07–449)
genotype: wild type
strain: B6CBAF1
Extracted molecule genomic DNA
Extraction protocol Male and female UGS were isolated separately and placed into 1x PBS containing 10% FCS on ice.
ChIP-seq experiments were performed as previously described in (10.1101/gad.281055.116). Briefly, they were fixed for 10 mn in 1% formaldehyde at room temperature and the crosslinking reaction was quenched with glycine. Subsequently, nuclei were extracted and chromatin was sheared using a water-bath sonicator (Covaris E220 evolution ultra-sonicator). Immunoprecipitation was done using the following anti- H3K27ac (Abcam, ab4729) or anti-H3K27me3 (Merck Millipore, 07–449). Libraries were prepared using the TruSeq protocol, and sequenced on the Illumina HiSeq system (100 bp single-end reads) according to manufactures instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024.
Raw ChIP-seq single-reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for single-reads and -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Truseq or Nextera adapters and bad quality bases.
Filtered reads were mapped on mm39 with bowtie2 version 2.4.5 with the default parameters. Only alignments with a mapping quality above 30 were kept (Samtools v1.16.1).
Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with with --call-summits -B (and --nomodel --extsize 200 for single-read). Coverages were normalized to million mapped reads/pairs.
Assembly: mm39
Supplementary files format and content: *narrowPeak.gz: peaks from MACS2
Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads
 
Submission date Dec 15, 2023
Last update date Apr 17, 2024
Contact name Aurelie Hintermann
E-mail(s) aur.hin@gmail.com
Organization name University of Geneva
Department Genetics and Evolution
Street address 30 quai Ernest-Ansermet
City Geneva
ZIP/Postal code 1205
Country Switzerland
 
Platform ID GPL21103
Series (2)
GSE250267 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS
GSE250367 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq]
Relations
BioSample SAMN38859256
SRA SRX22906488

Supplementary file Size Download File type/resource
GSM7977989_ChIP_H3K27me3_mm_E185_MUGS_rep1.bw 168.1 Mb (ftp)(http) BW
GSM7977989_ChIP_H3K27me3_mm_E185_MUGS_rep1.narrowPeak.gz 1.2 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA

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